GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydratase in Dinoroseobacter shibae DFL-12

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate 3607238 Dshi_0653 Prephenate dehydratase (RefSeq)

Query= BRENDA::Q9SA96
         (392 letters)



>FitnessBrowser__Dino:3607238
          Length = 280

 Score =  174 bits (441), Expect = 3e-48
 Identities = 112/285 (39%), Positives = 147/285 (51%), Gaps = 15/285 (5%)

Query: 106 VRISFQGIPGAYSETAALKAFPNCETVPCEQFEAAFQAVELWLVDKAVLPIENSVGGSIH 165
           ++I+FQG PGAYS  A   A P+ E VPC  FE  F AV     D  +LP+ENS  G + 
Sbjct: 3   LKIAFQGEPGAYSHQACHDARPDAEAVPCRTFEDVFAAVHDGSCDLGMLPVENSTYGRVA 62

Query: 166 RNYDLLLRHRLHIVQEVHLPVNHCLLGVPGVKKEDIKCVLSHPQALDQCVNSLNNLGIQR 225
             + LL    LHI++E  + V+  LL VPG K  DI+   SH   L QC + L    IQ 
Sbjct: 63  DIHRLLPESGLHIIEEAFVRVHINLLAVPGAKLGDIRTAQSHTVLLGQCRSFLRAHDIQP 122

Query: 226 ISAKDTATAAQTVSSSGKIDVGAIASVRAANIYGLDILAENIQDDVNNVTRFLILARE-P 284
           ++  DTA +A  V+  G     A+AS  A  IYGLD+LA +I+D  NN TRFLI+  E  
Sbjct: 123 VTGADTAGSAMHVAQEGNPAHAALASELAGEIYGLDVLARHIEDQDNNTTRFLIMTPELD 182

Query: 285 MIPRTDRPYKTSIVFSLEEGPGVLFKALAVFALRSINLSKIESRPQRRRPLRVVDGSNNG 344
           +  R      TS VF +   P  L+KA+  FA   +N++K+ES         +V GS   
Sbjct: 183 LTRRGSGKMITSFVFQVRNIPAALYKAMGGFATNGVNMTKLES--------YMVGGSFTA 234

Query: 345 SAKYFDYLFYIDFEASMADTRAQHALGHLQEFASFIRILGCYPMD 389
           +       FY D E    D   + AL  L  F S + ILG YP D
Sbjct: 235 TQ------FYADIEGHPDDANVRRALDELGYFTSQLEILGVYPAD 273


Lambda     K      H
   0.321    0.135    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 238
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 392
Length of database: 280
Length adjustment: 28
Effective length of query: 364
Effective length of database: 252
Effective search space:    91728
Effective search space used:    91728
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory